The Supreme Council of the Armed Forces (SCAF) has been ruling Egypt by decree since the fall of Hosni Mubarak in 2011. This week, however, the country got its first elected president after Mohamed Morsy, the candidate of the Muslim Brotherhood‘s Freedom and Justice Party, was declared the winner of a run-off. In the latest issue of TIME (available to subscribers here), Jay Newton-Small and Abigail Hauslohner examine the dynamics of the Egyptian military and SCAF and ponder how Morsy and the generals will get along. Hauslohner also filed the following report on the deteriorating human rights situation in the country–and the sometimes bizarre ways the generals have of explaining it away:

Heba Morayef, a researcher at the Human Rights Watch office in Cairo, remembers the one and only meeting her group has ever been granted with the generals (probably the last too, she laughs) in June of last year. General Mohamed El-Assar, a man with plenty of friends in Washington, was the most senior general in the room, she recalls, adding that it was an unusual moment of outreach for Egypt’s typically opaque armed forces. “They were certainly keen to receive us as one of the many foreign delegations coming through town,” she says. “And interestingly, they served us pumpkin pie. A lot of them referred to the fact that they had trained in the U.S. And they were like, ‘Would you like some pumpkin pie?’ It wasn’t the first time Morayef had met with Egyptian officers who had displayed such familiarity with American culture. In 2010 I went to a meeting with state security and they served us donuts. You can’t get donuts or pumpkin pie very easily in Cairo,” she says.

HRW was there to talk about what Morayef said were some very serious concerns. In less than five months of military rule, the junta had sent thousands of civilians to military trials, cracked down on critics in the bloggersphere, and tortured activists it had detained. Military police had even subjected a group of 17 women detainees to invasive “virginity tests.” “We went to discuss our concerns about the most serious human rights violations we were seeing at the time,” says Morayef. “We discussed military trials, the summoning of journalists, and torture and virginity tests.It’s not a discussion that went well, and I think reflected the fact that it was the first time that SCAF had met a human rights organization.”

In fact it was less a discussion than a series of speeches interspersed with shouting, she says. “It wasn’t a discussion, it was a two-way. They weren’t interested in listening to what we had to say. It was a very stilted conversation in which al-Assar would make long, stilted speeches and then the translator would translate even though al-Assar speaks very good English. They weren’t used to being criticized for their own direct involvement in abuses. And as far as we were concerned, we could only really recognize their role during [the February 2011 uprising] as a potentially positive–the fact that they didn’t use violence then–but then we went on to list all of our concerns. So most of the two-hour meeting was spent criticizing them. I think they really weren’t expecting that because they yelled at us on three occasions. They said, ‘We will not accept organizations from the outside coming and telling us what to do.'”

What’s odd, Morayef says, is that even in the final years of the Mubarak regime, which had long employed torture and excessive force against civilians, the regime had started to develop rhetoric to deal with their critics. “Mubarak’s information policy had shifted somewhat to say things like, ‘We’re looking into this’ or ‘these were isolated cases.’ Whereas the SCAF was much more 1960s-style absolute denial, even though there’s footage.” Mubarak had never allowed his generals to have much of a public profile. And after a year and a half in the seat of power, the junta is still grasping for the right words.

When former U.S. President Jimmy Carter met with SCAF Chairman Field Marshal Mohamed Hussein Tantawi in January, he brought up allegations of the military’s human rights abuses, including an incident captured on video that had recently gone viral. In the video, soldiers are seen beating and stripping a female protester of her black abaya, exposing the woman’s blue bra, as they broke up protests near Tahrir Square. “[Tantawi] basically denied that the blue bra incident had happened at all. And with a very straight face, he said that it was fabricated,” says a source with knowledge of the meeting. “[The generals] got very animated about it,” the source says. It was one of the only parts of the meeting that seemed to work them into a frenzy, all interrupting each other and denying the incident’s veracity in different ways. They clearly hadn’t worked out a unified message. “Some of them said, ‘look, the soldiers were actually helping her and the video had been manipulated.’ One of them said ‘the weather was so cold, why would she have been wearing so little anyway.'”

One thing the generals have figured out, however, is how to talk to members of the U.S. Congress, the American military and the White House. However, they may actually be more comfortable talking to Washington with than their own domestic audience. As Mubarak did, the generals habitually paint themselves, for example, as protectors of minorities like the country’s large Coptic Christian population. But Morayef says minorities may have actually suffered more in the past 16 months of military rule than in any year under Mubarak. And in some cases, the military has been directly involved in stoking sectarian tensions and violence against women.

“The short end of the story is that over the last year and a half, we’ve had people being tortured, whipped, beaten, kicked–as early as February 5, again on March 6, March 9, throughout last summer, December, and most recently in Abassiya,” says Morayef. “None of those cases of torture by the military have been investigated,” she says. And in most incidents they were flatly denied. The most notorious incident occurred on October 9, 2011 when the military crushed a demonstration led by Christian protesters, killing 24 people, 14 of whom were shot dead; some were run over by military vehicles. The military had crushed an earlier protest in Tahrir on March 9, 2011, arresting nearly 200 people, beating many of them and subjecting 17 women to forced virginity tests. Neither case has resulted in a conviction of a member of the armed forces, but activists have been detained at length.

The military has clamped down on freedom of expression in response to a population of critics that have only grown bolder since the uprising, according to Morayef. They tend to invoke the same laws that Mubarak had used to repress the media like Article 184 of the penal code (passed in 1937), which makes it a crime to insult “the army or the courts or the authorities.” The military is also particularly fond of Article 102 of the penal code that criminalizes the spreading of false information with the purpose of affecting public order or spreading fear or harming national interests. “What they mean by false information was, for example, [activist] Michael Nabil talking on his Facebook profile about the military being responsible for torture and virginity tests,” Morayef says. Another activist and blogger, Hossam al-Hamalawy, was summoned for military questioning after alleging that the head of military police, Hamdy Badeen, was personally responsible for torture. Other well known journalists and activists have been summoned as well. Later in 2011, SCAF amended the penal code with an article to make “thuggery”–a term now often applied to protesters–a crime. And earlier this month, ahead of the presidential run-off vote, the military-appointed Minister of Justice issued a decree authorizing its military police to arrest civilians under broadly defined circumstances to refer them to military trial. On June 25, an administrative court struck down that decree, but it remains unclear what kind of power the court wields in the face of the military.

Says Morayef: “We know from our experience in Chile and Mexico that military trials are fundamentally not independent and will cover up their own crimes. There has never been any accountability for military abuses.” More than 12,000 civilians have been sent to closed military trials since SCAF began running the country.